Genome‐wide association mapping and comparative genomics identifies genomic regions governing grain nutritional traits in finger millet (<i>Eleusine coracana</i> L. Gaertn.)

Puranik, Swati; Sahu, Pranav Pankaj; Beynon, Sarah; Srivastava, Rakesh K.; Sehgal, Deepmala; Ojulong, Henry; Yadav, Rattan

doi:10.1002/ppp3.10120

Cited by 67 publications

(59 citation statements)

References 79 publications

(114 reference statements)

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“…In foxtail millet, Jaiswal et al [ 40 ] identified 74 marker–trait associations for 10 micronutrient traits through GWAS. Recently, Puranik et al [ 42 ] performed GWAS in finger millet to identify 418 SNPs linked to micronutrient content. These studies should be extended to enable genomics-assisted breeding for the development of improved varieties with high micronutrient content.…”

Section: Mainstreaming Millets For Ensuring Multiple Securities Durinmentioning

confidence: 99%

Small Millets for Enduring Food Security Amidst Pandemics

Muthamilarasan

Prasad

2021

Trends in Plant Science

125

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Food security is an ongoing problem, and current staple foods are not sufficient to overcome challenges such as the present COVID-19 pandemic. We propose here that small millets have the potential to become new staple crops, especially in hunger hotspots. Currently, the absence of intensification of millet farming, lack of deployment of genetic tools for trait improvement, and the need for optimization of storage and supply chains limit crop production. We highlight a roadmap to strengthen small millet cultivation, such as identifying varieties suitable for particular environments and targeting trait improvement using genetic and genomic approaches. These approaches will help to combat hunger and malnutrition and also economically benefit the farmers and stakeholders involved in small millet cultivation amidst the ongoing pandemic.

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Section: Mainstreaming Millets For Ensuring Multiple Securities Durinmentioning

confidence: 99%

Small Millets for Enduring Food Security Amidst Pandemics

Muthamilarasan

Prasad

2021

Trends in Plant Science

125

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“…( 2014 ); Tiwari et al ( 2020 ) Two-pore channel ( TPC1 ), Ca2 + ATPase , Ca2 + /H + antiporter (CAX1), CaM, CBL, CIPK , and CDPK Uptake, translocation, and accumulation of calcium Calcium biofortification Sharma et al ( 2017 ); Sood et al, 2016 ; Mirza et al. ( 2014 ); Singh et al ( 2014 ) Prolamin‐binding factor DNA binding with one finger only ( PBF Dof ) Nitrogen transport and mobilization in the plant Nitrogen use efficiency Gupta et al ( 2013 ); Gupta et al, 2018 EcNRAMP2, EcNRAMP6, EcPDR9, and EcZTP29, NAM , mitochondrial 3-hydroxyisobutyrate dehydrogenase-like 1 Fe and Zn assimilation in finger millet under stress Fe and Zn biofortification Chandra et al ( 2020 ); Puranik et al ( 2020 ) 2 Foxtail millet Granule-bound starch synthase 1 Physicochemical properties of starch Amylose content Fukunaga et al. ( 2002 ); Bai et al.…”

Section: Deriving Innovations In the Traditional Mixed Cropping Systementioning

confidence: 99%

“…Among the three groups of plants, CAM shows the highest WUE followed by C4 plants (having twice the WUE of C3 species) and C3 plants, respectively. Water use efficiency of crops can be improved by selection of crops according to cropping systems based on available water supplies and increasing seasonal evapo-transpiration (Prihar et al 2000). In the traditional mixed cropping system (Barahnaja) crops are selected based on their stress tolerance and placed as per the availability of water in different fields.…”

Section: Improved Water and Nutrient Use Efficiencymentioning

confidence: 99%

Mainstreaming Barahnaja cultivation for food and nutritional security in the Himalayan region

et al. 2021

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Selective production of input intensive crops in the present scenario have resulted in productivity stagnation or even decline due to excessive usage of chemicals, affecting the farmers economically. Sustainable agriculture is the way to increase agricultural productivity and economic prosperity by protecting all natural resources. It maintains a balance of soil fertility with crop productivity and nutritional quality. The mixed cropping systems followed earlier in different regions according to their tradition, climatic zone, soil and water conditions were climate-smart approaches to sustainable food production based on practical experiences over the years of old generations. The life style changes, imbalance in farming system in last 70 years and demand for more food as well as declining land resources resulted in intensive agriculture. Besides, least returns and less demand of ethnic crops gave more preference to major staple food crops. Barahnaja is a traditional orphan crops based mixed cropping system practiced in Himalayan region due to its sustainability and assured crop harvest during erratic weather conditions. This traditional farming method is an exemplary scientific approach to derive innovations with respect to productivity, quality, plant soil interactions and organic agriculture. The main focus of the review is to substantiate the characteristics of the traditional mixed cropping system by describing the advantages of the system and opportunities for scientific innovation towards new knowledge and sustainability.

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“…However, again the accessions and/or molecular markers involved were generally limited to small numbers, and studies did not have available a finger millet genome assembly to map markers to chromosome positions. These studies include those of Dida et al (2021) who used a medium-sized panel of SNPs but only 52 East African accessions to search for blast disease resistance MTAs; Puranik et al (2020) who used a large panel of SNPs but assessed only 190 genotypes to search for grain nutrient-content-related MTAs; Sharma et al (2018) who applied a medium-sized panel of SNPs to only 113 accessions to search for MTAs in 14 agro-morphological traits; and Tiwari et al (2020) who, beginning with the same SNPs and germplasm panel of Sharma et al (2018), explored marker associations with grain protein content. Despite their limited scope, these previous studies indicated some MTAs.…”

Section: Characterization Of Finger Milletmentioning

confidence: 99%

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

Bančič

Odeny

et al. 2021

Preprint

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Advances in sequencing technologies mean that insights into crop diversification aiding future breeding can now be explored in crops beyond major staples. For the first time, we use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the sub-genome level. A set of 8,778 SNPs and 13 agronomic traits characterizing a broad panel of 423 landrace accessions from Africa and Asia suggested the crop has undergone complex, context-specific diversification consistent with a long domestication history. Both Principal Component Analysis and Discriminant Analysis of Principal Components of SNPs indicated four groups of accessions that coincided with the principal geographic areas of finger millet cultivation. East Africa, the considered origin of the crop, appeared the least genetically diverse. A Principal Component Analysis of phenotypic data also indicated clear geographic differentiation, but different relationships among geographic areas than genomic data. Neighbour-joining trees of sub-genomes A and B showed different features which further supported the crop’s complex evolutionary history. Our genome-wide association study indicated only a small number of significant marker-trait associations. We applied then clustering to marker effects from a ridge regression model for each trait which revealed two clusters of different trait complexity, with days to flowering and threshing percentage among simple traits, and finger length and grain yield among more complex traits. Our study provides comprehensive new knowledge on the distribution of genomic and phenotypic variation in finger millet, supporting future breeding intra- and inter-regionally across its major cultivation range.Core ideas8,778 SNPs and 13 agronomic traits characterized a panel of 423 finger millet landraces.4 clusters of accessions coincided with major geographic areas of finger millet cultivation.A comparison of phenotypic and genomic data indicated a complex diversification history.This was confirmed by the analysis of allotetraploid finger millet’s separate sub-genomes.Comprehensive new knowledge for intra- and inter-regional breeding is provided.

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Genome‐wide association mapping and comparative genomics identifies genomic regions governing grain nutritional traits in finger millet (Eleusine coracana L. Gaertn.)

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 67 publications

References 79 publications

Small Millets for Enduring Food Security Amidst Pandemics

Small Millets for Enduring Food Security Amidst Pandemics

Mainstreaming Barahnaja cultivation for food and nutritional security in the Himalayan region

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

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